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- PDB-2qjy: Crystal structure of rhodobacter sphaeroides double mutant with s... -

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Basic information

Entry
Database: PDB / ID: 2qjy
TitleCrystal structure of rhodobacter sphaeroides double mutant with stigmatellin and UQ2
Components
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
KeywordsOXIDOREDUCTASE / Cytochrome B / 8 TM helixces Cytochrome C1 / 1 c-term TM helix Rieske / 1 N-term TM helix
Function / homology
Function and homology information


respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane ...respiratory chain complex III / quinol-cytochrome-c reductase / ubiquinol-cytochrome-c reductase activity / respirasome / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / intracellular membrane-bounded organelle / heme binding / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome c1, transmembrane anchor, C-terminal / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b / : / : / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / Cytochrome c1 / Cytochrome C1 family / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Chem-LOP / STIGMATELLIN A / STRONTIUM ION / UBIQUINONE-2 / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit / Cytochrome c1
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEsser, L. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Inhibitor-complexed Structures of the Cytochrome bc1 from the Photosynthetic Bacterium Rhodobacter sphaeroides.
Authors: Esser, L. / Elberry, M. / Zhou, F. / Yu, C.A. / Yu, L. / Xia, D.
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
M: Cytochrome b
N: Cytochrome c1
O: Ubiquinol-cytochrome c reductase iron-sulfur subunit
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)620,44578
Polymers596,68718
Non-polymers23,75860
Water12,574698
1
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
D: Cytochrome b
E: Cytochrome c1
F: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,78425
Polymers198,8966
Non-polymers7,88819
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35820 Å2
ΔGint-432 kcal/mol
Surface area69660 Å2
MethodPISA, PQS
2
G: Cytochrome b
H: Cytochrome c1
I: Ubiquinol-cytochrome c reductase iron-sulfur subunit
J: Cytochrome b
K: Cytochrome c1
L: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,81926
Polymers198,8966
Non-polymers7,92420
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35780 Å2
ΔGint-441 kcal/mol
Surface area69930 Å2
MethodPISA, PQS
3
M: Cytochrome b
N: Cytochrome c1
O: Ubiquinol-cytochrome c reductase iron-sulfur subunit
P: Cytochrome b
Q: Cytochrome c1
R: Ubiquinol-cytochrome c reductase iron-sulfur subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,84227
Polymers198,8966
Non-polymers7,94621
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35830 Å2
ΔGint-441 kcal/mol
Surface area69690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)351.891, 147.042, 161.312
Angle α, β, γ (deg.)90.00, 104.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 3 types, 18 molecules ADGJMPBEHKNQCFILOR

#1: Protein
Cytochrome b /


Mass: 50157.539 Da / Num. of mol.: 6 / Mutation: S287R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petB, fbcB / Plasmid: pRKD418 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02761
#2: Protein
Cytochrome c1 /


Mass: 29373.953 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: fbcC / Plasmid: pRKD418 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IY11, UniProt: Q02760*PLUS
#3: Protein
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


Mass: 19916.322 Da / Num. of mol.: 6 / Mutation: V135S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: petA, fbcF / Plasmid: pRKD418 / Production host: Escherichia coli (E. coli) / Strain (production host): pRKD418 / References: UniProt: Q02762, quinol-cytochrome-c reductase

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Sugars , 1 types, 6 molecules

#9: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 9 types, 752 molecules

#4: Chemical
ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Sr
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical
ChemComp-SMA / STIGMATELLIN A


Mass: 514.650 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C30H42O7
#7: Chemical
ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#8: Chemical
ChemComp-UQ2 / UBIQUINONE-2


Mass: 318.407 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H26O4
#10: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe2S2
#11: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.69 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50 mM BisTris 7.2pH, 0.5% beta-octylglucoside, 0.1% sucrose mono caprate, 7% PEG400, 5-10 mM Sr nitrate, 105 Glycerol, 200 mM NaCl, 5 mM NaN3, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.75 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 10, 2006 / Details: mirrors
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 295863 / Num. obs: 293559 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 5 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 14.32
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 1.25 / Num. unique all: 23288 / Rsym value: 0.577 / % possible all: 74.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FYN

2fyn


Resolution: 2.4→18 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 6986056.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Complex NCS restraints (89)
RfactorNum. reflection% reflectionSelection details
Rfree0.251 4924 1.7 %SHELLS
Rwork0.226 ---
all0.237 290327 --
obs0.226 290127 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.972 Å2 / ksol: 0.341076 e/Å3
Displacement parametersBiso mean: 70.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.67 Å20 Å2-13.83 Å2
2---7.17 Å20 Å2
3---14.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.4→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40398 0 1560 698 42656
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.68
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.11
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it3.162
X-RAY DIFFRACTIONc_scbond_it2.92
X-RAY DIFFRACTIONc_scangle_it4.092.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.344 613 1.5 %
Rwork0.344 39198 -
obs--77.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_MET.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3Ligand.parLigand.top
X-RAY DIFFRACTION4cis_peptide.paramwater.top
X-RAY DIFFRACTION5water_rep.param

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